From BioJava

How to Read a Fasta File with Biojava3

import java.io.File;
import java.io.FileInputStream;
import java.util.LinkedHashMap;
import java.util.Map.Entry;
 
import org.biojava3.core.sequence.ProteinSequence;
import org.biojava3.core.sequence.compound.AminoAcidCompound;
import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
import org.biojava3.core.sequence.io.FastaReader;
import org.biojava3.core.sequence.io.FastaReaderHelper;
import org.biojava3.core.sequence.io.GenericFastaHeaderParser;
import org.biojava3.core.sequence.io.ProteinSequenceCreator;
 
public class FastaOpen {
 
	public static void main(String[] args) throws Exception{
		/*
		 * Method 1: With the FastaReaderHelper
		 */
		//Try with the FastaReaderHelper
		LinkedHashMap<String, ProteinSequence> a = FastaReaderHelper.readFastaProteinSequence(new File(args[0]));
		//FastaReaderHelper.readFastaDNASequence for DNA sequences
 
		for (  Entry<String, ProteinSequence> entry : a.entrySet() ) {
			System.out.println( entry.getValue().getOriginalHeader() + "=" + entry.getValue().getSequenceAsString() );
		}
 
		/*
		 * Method 2: With the FastaReader Object 
		 */		
		//Try reading with the FastaReader
		FileInputStream inStream = new FileInputStream( args[0] );
		FastaReader<ProteinSequence,AminoAcidCompound> fastaReader = 
			new FastaReader<ProteinSequence,AminoAcidCompound>(
					inStream, 
					new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>(), 
					new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
		LinkedHashMap<String, ProteinSequence> b = fastaReader.process();
		for (  Entry<String, ProteinSequence> entry : b.entrySet() ) {
			System.out.println( entry.getValue().getOriginalHeader() + "=" + entry.getValue().getSequenceAsString() );
		}
	}
 
}